12-108562647-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_213595.4(ISCU):c.25C>T(p.Leu9=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000199 in 1,463,440 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. L9L) has been classified as Benign.
Frequency
Consequence
NM_213595.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ISCU | NM_213595.4 | c.25C>T | p.Leu9= | synonymous_variant | 1/5 | ENST00000311893.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ISCU | ENST00000311893.14 | c.25C>T | p.Leu9= | synonymous_variant | 1/5 | 1 | NM_213595.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000493 AC: 75AN: 152194Hom.: 0 Cov.: 37
GnomAD3 exomes AF: 0.000696 AC: 56AN: 80468Hom.: 0 AF XY: 0.000623 AC XY: 29AN XY: 46514
GnomAD4 exome AF: 0.000165 AC: 216AN: 1311134Hom.: 0 Cov.: 35 AF XY: 0.000149 AC XY: 96AN XY: 644932
GnomAD4 genome AF: 0.000492 AC: 75AN: 152306Hom.: 0 Cov.: 37 AF XY: 0.000658 AC XY: 49AN XY: 74466
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at